java的setquality值多少_Java SAMRecord.setBaseQualityString方法代码示例

import htsjdk.samtools.SAMRecord; //导入方法依赖的package包/类

public SAMRecord transfer(final BasicSamRecord basicSamRecord) {

final SAMRecord samRecord =

samRecordFactory.createSAMRecord(this.mFileHeader);

samRecord.setValidationStringency(this.validationStringency);

samRecord.setHeader(this.mFileHeader);

samRecord.setReadName(basicSamRecord.readName());

samRecord.setFlags(basicSamRecord.flag());

if (!basicSamRecord.contigName().equals("*")) {

samRecord.setReferenceName(basicSamRecord.contigName());

}

samRecord.setAlignmentStart(basicSamRecord.position());

samRecord.setMappingQuality(basicSamRecord.mapQ());

samRecord.setCigarString(basicSamRecord.cigar());

if (basicSamRecord.contigId() != FAKE_CONTIG_ID) {

samRecord.setMateReferenceName(basicSamRecord.mateContigName());

samRecord.setMateAlignmentStart(basicSamRecord.matePosition());

samRecord.setInferredInsertSize(basicSamRecord.infferdSize());

}

byte[] quality = null;

if (basicSamRecord.quality().length == 1 && basicSamRecord.quality()[0] == '*') {

samRecord.setBaseQualities(SAMRecord.NULL_QUALS);

} else {

quality = basicSamRecord.quality();

if (basicSamRecord.compressFlag()) {

quality = QualityCompressTools.deCompressQual(quality);

}

}

byte[] sequence = null;

if (basicSamRecord.sequence().length == 1 && basicSamRecord.sequence()[0] == '*') {

samRecord.setReadBases(SAMRecord.NULL_SEQUENCE);

} else {

sequence = basicSamRecord.sequence();

if (basicSamRecord.compressFlag()) {

sequence = BaseCompressTools.decompressBase(sequence, quality);

}

// 必须在执行之后解压之后再赋值，因为解压可能会导致quality变化。

samRecord.setBaseQualityString(new String(quality));

samRecord.setReadString(new String(sequence));

}

List tmp = CollectionConverter.asJavaList(basicSamRecord.attributeList());

for (String attribute : tmp) {

parseTag(samRecord, attribute);

}

return samRecord;

}